First thing I would think is carburetor. Does the splutter hit whether you're pulling or cruising?
Carburetor rebuilds that miss the problem is probably the number one repair that needs to be redone. Not picking on your mechanical skills, not at all. That is just one of those jobs........ use a piece of wire or fishing line or welding tip cleaner and run the ports to make for sure and for certain they are all open and clean. Double check every measurement of float height, linkage bends and so on. Gotta be perfect. Also look careful to make sure the throttle plate shaft hoes aren't wearing open. Ski boats tend to run the same throttle position all the time and the shaft can wear a spot on the housing that leaks.
Everyone is going to tell you not to use automotive fuel filters, so might as well start that ball rolling. Automotive inline filters not only unsafe but illegal in a boat. You want and really need a spin on marine canister filter with water separator capability. Take out the automotive filters and make sure to use only marine rated fuel line.
Double check timing. You should see around 24-26? advance when you spin up past 2k. Make sure the advance is working correctly.